Hfq binds ribonucleotides in three different RNA-binding sites

Modulation of Pseudomonas aeruginosa quorum sensing by ajoene through direct competition with small RNAs for binding at the proximal site of Hfq - a structure-based perspective

Bacteria can communicate to each other via quorum sensing, a cell density-dependent gene regulation system that stimulates the expression of virulence factors in the neighboring cells. Although the interaction of the natural product ajoene with the Hfq protein has been associated with the disruption of the quorum sensing system in Pseudomonas aeruginosa, there is no information concerning the corresponding ligand-target interaction process. Herein we observed a strong correlation (p < 0.00001) between the estimated affinities for the binding of 23 ajoene analogues at the proximal site of the Hfq protein of P. aeruginosa and their corresponding IC₅₀ values, which reflect the reduction in the transcription of a virulence factor after quorum sensing inhibition. In this concern, our analyses reinforces previous propositions suggesting that ajoene could target the Hfq protein and affects its interaction with RNAs. Based on docking simulations, we tried to elucidate the binding mode of ajoene into the proximal Hfq site and the also to established the minimum set of groups that would be necessary for a good interaction at this site, which includes a single hydrogen bond acceptor feature surrounded by groups that interact via π-sulfur (i.e., disulfide sulfurs) and/or π-alkyl/π-π stacking interactions (e.g., vinyl or small aryl/heteroaryl/heterocyclic groups). Because of the widespread role of Hfq as a matchmaker between messenger and small regulatory RNAs in Gram-negatives, we believe the discussion here provided for P. aeruginosa could be extrapolated for Gram-negatives in general, while the interaction of ajoene over the Hfq protein of Gram-positives would still remain more controversial.

Structural Investigations of RNA–Protein Complexes in Post-Ribosomal Era

Abstract

Structural studies of RNA–protein complexes are important for understanding many molecular mechanisms occurring in cells (e.g., regulation of protein synthesis and RNA-chaperone activity of proteins). Various objects investigated at the Institute of Protein Research of the Russian Academy of Sciences are considered. Based on the analysis of the structures of the complexes of the ribosomal protein L1 with specific regions on both mRNA and rRNA, the principles of regulation of the translation of the mRNA of its own operon are presented. The studies of the heterotrimeric translation initiation factor IF2 of archaea and eukaryotes are described, and the data on the interaction of glycyl-tRNA-synthetase with viral IRES are reported. The results of studying the interaction of RNA molecules with one of functionally important sites of the Hfq protein are presented, and the differences in the RNA-binding properties of the Hfq and archaeal Lsm proteins are revealed.

Specific and Global RNA Regulators in Pseudomonas aeruginosa

Pseudomonas aeruginosa (Pae) is an opportunistic pathogen showing a high intrinsic resistance to a wide variety of antibiotics. It causes nosocomial infections that are particularly detrimental to immunocompromised individuals and to patients suffering from cystic fibrosis. We provide a snapshot on regulatory RNAs of Pae that impact on metabolism, pathogenicity and antibiotic susceptibility. Different experimental approaches such as in silico predictions, co-purification with the RNA chaperone Hfq as well as high-throughput RNA sequencing identified several hundreds of regulatory RNA candidates in Pae. Notwithstanding, using in vitro and in vivo assays, the function of only a few has been revealed. Here, we focus on well-characterized small base-pairing RNAs, regulating specific target genes as well as on larger protein-binding RNAs that sequester and thereby modulate the activity of translational repressors. As the latter impact large gene networks governing metabolism, acute or chronic infections, these protein-binding RNAs in conjunction with their cognate proteins are regarded as global post-transcriptional regulators.

Structure and RNA-Binding Properties of Lsm Protein from Halobacterium salinarum

The structure and the RNA-binding properties of the Lsm protein from Halobacterium salinarum have been determined. A distinctive feature of this protein is the presence of a short L4 loop connecting the β3 and β4 strands. Since bacterial Lsm proteins (also called Hfq proteins) have a short L4 loop and form hexamers, whereas archaeal Lsm proteins (SmAP) have a long L4 loop and form heptamers, it has been suggested that the length of the L4 loop may affect the quaternary structure of Lsm proteins. Moreover, the L4 loop covers the region of SmAP corresponding to one of the RNA-binding sites in Hfq, and thus can affect the RNA-binding properties of the protein. Our results show that the SmAP from H. salinarum forms heptamers and possesses the same RNA-binding properties as homologous proteins with the long L4 loop. Therefore, the length of the L4 does not govern the number of monomers in the protein particles and does not affect the RNA-binding properties of Lsm proteins.

Stabilization of Hfq-mediated translational repression by the co-repressor Crc in Pseudomonas aeruginosa

In Pseudomonas aeruginosa the RNA chaperone Hfq and the catabolite repression control protein (Crc) govern translation of numerous transcripts during carbon catabolite repression. Here, Crc was shown to enhance Hfq-mediated translational repression of several mRNAs. We have developed a single-molecule fluorescence assay to quantitatively assess the cooperation of Hfq and Crc to form a repressive complex on a RNA, encompassing the translation initiation region and the proximal coding sequence of the P. aeruginosa amiE gene. The presence of Crc did not change the amiE RNA-Hfq interaction lifetimes, whereas it changed the equilibrium towards more stable repressive complexes. This observation is in accord with Cryo-EM analyses, which showed an increased compactness of the repressive Hfq/Crc/RNA assemblies. These biophysical studies revealed how Crc protein kinetically stabilizes Hfq/RNA complexes, and how the two proteins together fold a large segment of the mRNA into a more compact translationally repressive structure. In fact, the presence of Crc resulted in stronger translational repression in vitro and in a significantly reduced half-life of the target amiE mRNA in vivo. Although Hfq is well-known to act with small regulatory RNAs, this study shows how Hfq can collaborate with another protein to down-regulate translation of mRNAs that become targets for the degradative machinery.

Diversity of LSM Family Proteins: Similarities and Differences

Members of the Lsm protein family are found in all three domains of life: bacteria, archaea, and eukarya. They are involved in numerous processes associated with RNA processing and gene expression regulation. A common structural feature of all Lsm family proteins is the presence of the Sm fold consisting of a five-stranded β-sheet and an α-helix at the N-terminus. Heteroheptameric eukaryotic Sm and Lsm proteins participate in the formation of spliceosomes and mRNA decapping. Homohexameric bacterial Lsm protein, Hfq, is involved in the regulation of transcription of different mRNAs by facilitating their interactions with small regulatory RNAs. Furthermore, recently obtained data indicate a new role of Hfq as a ribosome biogenesis factor, as it mediates formation of the productive structure of the 17S rRNA 3'- and 5'-sequences, facilitating their further processing by RNases. Lsm archaeal proteins (SmAPs) form homoheptamers and likely interact with single-stranded uridine-rich RNA elements, although the role of these proteins in archaea is still poorly understood. In this review, we discuss the structural features of the Lsm family proteins from different life domains and their structure-function relationships.

Dynamic interactions between the RNA chaperone Hfq, small regulatory RNAs, and mRNAs in live bacterial cells

RNA-binding proteins play myriad roles in regulating RNAs and RNA-mediated functions. In bacteria, the RNA chaperone Hfq is an important post-transcriptional gene regulator. Using live-cell super-resolution imaging, we can distinguish Hfq binding to different sizes of cellular RNAs. We demonstrate that under normal growth conditions, Hfq exhibits widespread mRNA-binding activity, with the distal face of Hfq contributing mostly to the mRNA binding in vivo. In addition, sRNAs can either co-occupy Hfq with the mRNA as a ternary complex, or displace the mRNA from Hfq in a binding face-dependent manner, suggesting mechanisms through which sRNAs rapidly access Hfq to induce sRNA-mediated gene regulation. Finally, our data suggest that binding of Hfq to certain mRNAs through its distal face can recruit RNase E to promote turnover of these mRNAs in a sRNA-independent manner, and such regulatory function of Hfq can be decoyed by sRNA competitors that bind strongly at the distal face.

Messenger RNAs or mRNAs are molecules that the cell uses to transfer the information stored in the cell’s DNA so it can be used to make proteins. Bacteria can regulate their levels of mRNA molecules, and they can therefore control how many proteins are being made, by producing a different type of RNA called small regulatory RNAs or sRNAs. Each sRNA can bind to several specific mRNA targets, and lead to their degradation by an enzyme called RNase E. Certain bacterial RNA-binding proteins, such as Hfq, protect sRNAs from being degraded, and help them find their mRNA targets.

Hfq is abundant in bacteria. It is critical for bacterial growth under harsh conditions and it is involved in the process through which pathogenic bacteria infect cells. However, it is outnumbered by the many different RNA molecules in the cell, which compete for binding to the protein. It is not clear how Hfq prioritizes the different RNAs, or how binding to Hfq alters RNA regulation. Park, Prévost et al. imaged live bacterial cells to see how Hfq binds to RNA strands of different sizes.

The experiments revealed that, when bacteria are growing normally, Hfq is mainly bound to mRNA molecules, and it can recruit RNase E to speed up mRNA degradation without the need for sRNAs. Park, Prévost et al. also showed that sRNAs could bind to Hfq by either replacing the bound mRNA or co-binding alongside it. The sRNA molecules that strongly bind Hfq can compete against mRNA for binding, and thus slow down the degradation of certain mRNAs.

Hfq could be a potential drug target for treating bacterial infections. Understanding how it interacts with other molecules in bacteria could provide help in the development of new therapeutics. These findings suggest that a designed RNA that binds strongly to Hfq could disrupt its regulatory roles in bacteria, killing them. This could be a feasible drug design opportunity to counter the emergence of antibiotic-resistant bacteria.

Use of Fluorescent Nucleotides to Map RNA-Binding Sites on Protein Surface

Currently, studies of RNA/protein interactions occupy a prominent place in molecular biology and medicine. The structures of RNA-protein complexes may be determined by X-ray crystallography or NMR for further analyses. These methods are time-consuming and difficult due to the versatility and dynamics of the RNA structure. Furthermore, due to the need to solve the "phase problem" for each dataset in crystallography, crystallographic structures of RNA are still underrepresented. Structure determination of single ribonucleotide-protein complexes is a useful tool to identify the position of single-stranded RNA-binding sites in proteins. We describe here a structural approach that incorporates affinity measurement of a protein for various single ribonucleotides, ranking the RNA/protein complexes according to their stability. This chapter describes how to perform these measurements, including a perspective for the analysis of RNA-binding sites in protein and single-nucleotide crystal soaking.

Distinctive Regulation of Carbapenem Susceptibility in Pseudomonas aeruginosa by Hfq

Carbapenems are often the antibiotics of choice to combat life threatening infections caused by the opportunistic human pathogen Pseudomonas aeruginosa. The outer membrane porins OprD and OpdP serve as entry ports for carbapenems. Here, we report that the RNA chaperone Hfq governs post-transcriptional regulation of the oprD and opdP genes in a distinctive manner. Hfq together with the recently described small regulatory RNAs (sRNAs) ErsA and Sr0161 is shown to mediate translational repression of oprD, whereas opdP appears not to be regulated by sRNAs. At variance, our data indicate that opdP is translationally repressed by a regulatory complex consisting of Hfq and the catabolite repression protein Crc, an assembly known to be key to carbon catabolite repression in P. aeruginosa. The regulatory RNA CrcZ, which is up-regulated during growth of P. aeruginosa on less preferred carbon sources, is known to sequester Hfq, which relieves Hfq-mediated translational repression of genes. The differential carbapenem susceptibility during growth on different carbon sources can thus be understood in light of Hfq-dependent oprD/opdP regulation and of the antagonizing function of the CrcZ RNA on Hfq regulatory complexes.

Crystal structures and RNA-binding properties of Lsm proteins from archaea Sulfolobus acidocaldarius and Methanococcus vannielii: Similarity and difference of the U-binding mode

Sm and Sm-like (Lsm) proteins are considered as an evolutionary conserved family involved in RNA metabolism in organisms from bacteria and archaea to human. Currently, the function of Sm-like archaeal proteins (SmAP) is not well understood. Here, we report the crystal structures of SmAP proteins from Sulfolobus acidocaldarius and Methanococcus vannielii and a comparative analysis of their RNA-binding sites. Our data show that these SmAPs have only a uridine-specific RNA-binding site, unlike their bacterial homolog Hfq, which has three different RNA-binding sites. Moreover, variations in the amino acid composition of the U-binding sites of the two SmAPs lead to a difference in protein affinity for oligo(U) RNA. Surface plasmon resonance data and nucleotide-binding analysis confirm the high affinity of SmAPs for uridine nucleotides and oligo(U) RNA and the reduced affinity for adenines, guanines, cytidines and corresponding oligo-RNAs. In addition, we demonstrate that MvaSmAP1 and SacSmAP2 are capable of melting an RNA hairpin and, apparently, promote its interaction with complementary RNA.

Vibrio cholerae YaeO is a Structural Homologue of RNA Chaperone Hfq that Inhibits Rho-dependent Transcription Termination by Dissociating its Hexameric State

Rho-dependent transcription termination is a well-conserved process in bacteria. The Psu and YaeO proteins are the two established inhibitors of the ATP-dependent RNA helicase Rho protein of Escherichia coli. Here, we show a detailed sequence and phylogenetic analysis demonstrating that Vibrio cholerae YaeO (VcYaeO) is significantly distinct from its E. coli counterpart. VcYaeO induces significant growth defect on in vivo expression and inhibits in vitro functions of the V. cholerae Rho on directly binding to the latter. Through various biophysical techniques, we showed that interaction of VcYaeO disrupts the oligomeric state of the VcRho. Structure of VcYaeO solved at 1.75 Å resolution, the first crystal structure of a YaeO protein, demonstrates a beta-sandwich fold distinct from the NMR structure of the EcYaeO. Interestingly, VcYaeO structurally resembles the Hfq protein, and like the latter, it exhibits ssDNA/RNA-binding properties. Docking studies demonstrate probable interactions of VcYaeO with VcRho and mode of inhibition of RNA binding to Rho. We propose that VcYaeO inhibits the function of the Rho protein via disruption of the latter's hexameric assembly and also likely by sequestering the RNA from the Rho primarybinding sites.

Producing Hfq/Sm Proteins and sRNAs for Structural and Biophysical Studies of Ribonucleoprotein Assembly

Hfq is a bacterial RNA-binding protein that plays key roles in the post-transcriptional regulation of gene expression. Like other Sm proteins, Hfq assembles into toroidal discs that bind RNAs with varying affinities and degrees of sequence specificity. By simultaneously binding to a regulatory small RNA (sRNA) and an mRNA target, Hfq hexamers facilitate productive RNA∙∙∙RNA interactions; the generic nature of this chaperone-like functionality makes Hfq a hub in many sRNA-based regulatory networks. That Hfq is crucial in diverse cellular pathways-including stress response, quorum sensing, and biofilm formation-has motivated genetic and "RNAomic" studies of its function and physiology (in vivo), as well as biochemical and structural analyses of Hfq∙∙∙RNA interactions (in vitro). Indeed, crystallographic and biophysical studies first established Hfq as a member of the phylogenetically conserved Sm superfamily. Crystallography and other biophysical methodologies enable the RNA-binding properties of Hfq to be elucidated in atomic detail, but such approaches have stringent sample requirements, viz.: reconstituting and characterizing an Hfq·RNA complex requires ample quantities of well-behaved (sufficient purity, homogeneity) specimens of Hfq and RNA (sRNA, mRNA fragments, short oligoribonucleotides, or even single nucleotides). The production of such materials is covered in this chapter, with a particular focus on recombinant Hfq proteins for crystallization experiments.

Small Alarmone Synthetases as novel bacterial RNA-binding proteins

The alarmone nucleotides guanosine pentaphosphate (pppGpp) and tetraphosphate (ppGpp), collectively referred to as (p)ppGpp, are key regulators of bacterial growth, stress adaptation, antibiotic tolerance and pathogenicity. We have recently shown that the Small Alarmone Synthetase (SAS) RelQ from the Gram-positive pathogen Enterococcus faecalis has an RNA-binding activity (Beljantseva et al. 2017). RelQ's activities as an enzyme and as an RNA-binding protein are mutually incompatible: binding of single-stranded RNA potently inhibits (p)ppGpp synthesis in a sequence-specific manner, and RelQ's enzymatic activity destabilizes the RNA:RelQ complex. RelQ's allosteric regulator, pppGpp, destabilizes RNA binding and activates RelQ's enzymatic activity. Since SAS enzymes are widely distributed in bacteria, and, as has been discovered recently, are also mobilized by phages (Dedrick et al. 2017), RNA binding to SASs could be a widespread mechanism. The initial discovery raises numerous questions regarding RNA-binding function of the SAS enzymes: What is the molecular mechanism underlying the incompatibility of RNA:SAS complex formation with pppGpp binding and (p)ppGpp synthesis? What are the RNA targets in living cells? What is the regulatory output of the system - (p)ppGpp synthesis, modulation of RNA structure and function, or both?

An Experimental Tool to Estimate the Probability of a Nucleotide Presence in the Crystal Structures of the Nucleotide-Protein Complexes

A correlation between the ligand-protein affinity and the identification of the ligand in the experimental electron density maps obtained by X-ray crystallography has been tested for a number of RNA-binding proteins. Bacterial translation regulators ProQ, TRAP, Rop, and Hfq together with their archaeal homologues SmAP have been used. The equilibrium dissociation constants for the N-methyl-anthraniloyl-labelled adenosine and guanosine monophosphates titrated by the proteins have been determined by the fluorescent anisotropy measurements. The estimated stability of the nucleotide-protein complexes has been matched with a presence of the nucleotides in the structures of the proposed nucleotide-protein complexes. It has been shown that the ribonucleotides can be definitely identified in the experimental electron density maps at equilibrium dissociation constant <10 μM. At K_D of 20-40 μM, long incubation of the protein crystals in the nucleotide solution is required to obtain the structures of the complexes. The complexes with K_D value higher than 50 μM are not stable enough to survive in crystallization conditions.

Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: conservation of the lateral RNA-binding mode

The host factor Hfq, as the bacterial branch of the Sm family, is an RNA-binding protein involved in the post-transcriptional regulation of mRNA expression and turnover. Hfq facilitates pairing between small regulatory RNAs (sRNAs) and their corresponding mRNA targets by binding both RNAs and bringing them into close proximity. Hfq homologs self-assemble into homo-hexameric rings with at least two distinct surfaces that bind RNA. Recently, another binding site, dubbed the `lateral rim', has been implicated in sRNA·mRNA annealing; the RNA-binding properties of this site appear to be rather subtle, and its degree of evolutionary conservation is unknown. An Hfq homolog has been identified in the phylogenetically deep-branching thermophile Aquifex aeolicus (Aae), but little is known about the structure and function of Hfq from basal bacterial lineages such as the Aquificae. Therefore, Aae Hfq was cloned, overexpressed, purified, crystallized and biochemically characterized. Structures of Aae Hfq were determined in space groups P1 and P6, both to 1.5 Å resolution, and nanomolar-scale binding affinities for uridine- and adenosine-rich RNAs were discovered. Co-crystallization with U6 RNA reveals that the outer rim of the Aae Hfq hexamer features a well defined binding pocket that is selective for uracil. This Aae Hfq structure, combined with biochemical and biophysical characterization of the homolog, reveals deep evolutionary conservation of the lateral RNA-binding mode, and lays a foundation for further studies of Hfq-associated RNA biology in ancient bacterial phyla.

Functional analyses of putative PalS (Palindromic Self-recognition) motifs in bacterial Hfq

The bacterial protein Hfq has been linked to nucleic acid metabolism and signaling, however its explicit role has been elusive. Recently it was proposed that the C-termini of Hfq subunits in Hfq₆ complexes could be involved in functional interactions with other Hfq hexamers and/or nucleic acids. To test the proposed model of the native Hfq complex experimentally, we genetically engineered chimeric Hfq₆ complexes, in which C-termini of bacterial Hfq subunits were substituted with a sequence derived from human histone H2B (hH2B) that includes multiple functionally significant amino acids whose modifications have been linked to carcinogenesis. We demonstrate that this substitution results in an enhanced formation of dodecameric assemblies by the Hfq-hH2B hybrid - a result pointing to the possibility of a (functional) homology between these motifs in proteins from distant kingdoms. We hypothesize that these putative Palindromic Self-recognition (PalS) motifs could act as proteins' 'cohesive ends' that could allow the protein complexes carrying such motifs to interact dynamically and dissociate-reassociate in response to stress and/or growth phase-specific changes. We provide experimental support to the latter hypothesis and demonstrate that in E. coli the dodecameric Hfq assemblies are formed in a growth stage-specific manner. We describe a refined system - consisting solely of purified Hfq, polynucleotide phosporylase (PNP) and ADP - that allows reconstitution in vitro of characteristic 'SDS-insensitive' Hfq₆-Hfq₆ assemblies observed in experiments with whole-cell extracts obtained from exponentially-growing cells. We also optimized conditions for the extraction of intact native dodecameric Hfq complexes.

Bacterial Small Regulatory RNAs and Hfq Protein

Small regulatory RNA (sRNA) is a unique noncoding RNA involved in regulation of gene expression in both eukaryotic and bacterial cells. This short review discusses examples of positive and negative translation regulation by sRNAs in bacteria and participation of Hfq in these processes. The importance of structure investigation of nucleotide-protein and RNA-protein complexes for designing a model of Hfq interaction with both mRNA and sRNA simultaneously is demonstrated.

Characterization of RNA-binding properties of the archaeal Hfq-like protein from Methanococcus jannaschii

The Sm and Sm-like proteins are widely distributed among bacteria, archaea and eukarya. They participate in many processes related to RNA-processing and regulation of gene expression. While the function of the bacterial Lsm protein Hfq and eukaryotic Sm/Lsm proteins is rather well studied, the role of Lsm proteins in Archaea is investigated poorly. In this work, the RNA-binding ability of an archaeal Hfq-like protein from Methanococcus jannaschii has been studied by X-ray crystallography, anisotropy fluorescence and surface plasmon resonance. It has been found that MjaHfq preserves the proximal RNA-binding site that usually recognizes uridine-rich sequences. Distal adenine-binding and lateral RNA-binding sites show considerable structural changes as compared to bacterial Hfq. MjaHfq did not bind mononucleotides at these sites and would not recognize single-stranded RNA as its bacterial homologues. Nevertheless, MjaHfq possesses affinity to poly(A) RNA that seems to bind at the unstructured positive-charged N-terminal tail of the protein.

Hfq: the flexible RNA matchmaker

The RNA chaperone protein Hfq is critical to the function of small, base pairing RNAs in many bacteria. In the past few years, structures and modeling of wild type Hfq and assays of various mutants have documented that the homohexameric Hfq ring can contact RNA at four sites (proximal face, distal face, rim and C-terminal tail) and that different RNAs bind to these sites in various configurations. These studies together with novel in vitro and in vivo experimental approaches are beginning to give mechanistic insights into how Hfq acts to promote small RNA-mRNA pairing and indicate that flexibility is integral to the Hfq role in RNA matchmaking.

Sm-like protein Hfq: Composition of the native complex, modifications, and interactions

The bacterial Sm-like protein Hfq has been linked functionally to reactions that involve RNA; however, its explicit role and primary cellular localization remain elusive. We carried out a detailed biochemical characterization of native Escherichia coli Hfq obtained through methods that preserve its posttranslational modifications. ESI-MS analyses indicate modifications in 2-3 subunits/hexamer with a molecular mass matching that of an oxidized C:18 lipid. We show that the majority of cellular Hfq cannot be extracted without detergents and that purified Hfq can be retained on hydrophobic matrices. Analyses of purified Hfq and the native Hfq complexes observed in whole-cell E. coli extracts indicate the existence of dodecameric assemblies likely stabilized by interlocking C-terminal polypeptides originating from separate Hfq hexamers and/or accessory nucleic acid. We demonstrate that cellular Hfq is redistributed between transcription complexes and an insoluble fraction that includes protein complexes harboring polynucleotide phosphorylase (PNP). This distribution pattern is consistent with a function at the interface of the apparatuses responsible for synthesis and degradation of RNA. Taken together with the results of prior studies, these results suggest that Hfq could function as an anchor/coupling factor responsible for de-solubilization of RNA and its tethering to the degradosome complex.

Structural insights into the recognition of the internal A-rich linker from OxyS sRNA by Escherichia coli Hfq

Small RNA OxyS is induced during oxidative stress in Escherichia coli and it is an Hfq-dependent negative regulator of mRNA translation. OxyS represses the translation of fhlA and rpoS mRNA, which encode the transcriptional activator and σ^s subunit of RNA polymerase, respectively. However, little is known regarding how Hfq, an RNA chaperone, interacts with OxyS at the atomic level. Here, using fluorescence polarization and tryptophan fluorescence quenching assays, we verified that the A-rich linker region of OxyS sRNA binds Hfq at its distal side. We also report two crystal structures of Hfq in complex with A-rich RNA fragments from this linker region. Both of these RNA fragments bind to the distal side of Hfq and adopt a different conformation compared with those previously reported for the (A-R-N)_n tripartite recognition motif. Furthermore, using fluorescence polarization, electrophoresis mobility shift assays and in vivo translation assays, we found that an Hfq mutant, N48A, increases the binding affinity of OxyS for Hfq in vitro but is defective in the negative regulation of fhlA translation in vivo, suggesting that the normal function of OxyS depends on the details of the interaction with Hfq that may be related to the rapid recycling of Hfq in the cell.

Recognition of the small regulatory RNA RydC by the bacterial Hfq protein

Bacterial small RNAs (sRNAs) are key elements of regulatory networks that modulate gene expression. The sRNA RydC of Salmonella sp. and Escherichia coli is an example of this class of riboregulators. Like many other sRNAs, RydC bears a ‘seed’ region that recognises specific transcripts through base-pairing, and its activities are facilitated by the RNA chaperone Hfq. The crystal structure of RydC in complex with E. coli Hfq at a 3.48 Å resolution illuminates how the protein interacts with and presents the sRNA for target recognition. Consolidating the protein–RNA complex is a host of distributed interactions mediated by the natively unstructured termini of Hfq. Based on the structure and other data, we propose a model for a dynamic effector complex comprising Hfq, small RNA, and the cognate mRNA target.

DOI:http://dx.doi.org/10.7554/eLife.05375.001

A crucial step in the production of proteins is the translation of messenger RNA molecules. Other RNA molecules called small RNAs are also involved in this process: these small RNAs bind to the messenger RNA molecules to either increase or decrease the production of proteins.

Bacteria and other microorganisms use small RNA molecules to help them respond to stress conditions and to changes in their environment, such as fluctuations in temperature or the availability of nutrients. The ability to rapidly adapt to these changes enables bacteria to withstand harmful conditions and to make efficient use of resources available to them.

Many small RNA molecules use a protein called Hfq to help them interact with their target messenger RNAs. In some cases this protein protects the small RNA molecules when they are not bound to their targets. Hfq also helps the small RNA to bind to the messenger RNA, and then recruits other enzymes that eventually degrade the complex formed by the different RNA molecules.

Previous research has shown that six Hfq subunits combine to form a ring-shaped structure and has also provided some clues about the way in which Hfq can recognise a short stretch of a small RNA molecule, but the precise details of the interaction between them are not fully understood. Now Dimastrogiovanni et al. have used a technique called X-ray crystallography to visualize the interaction between Hfq and a small RNA molecule called RydC.

These experiments reveal that a particular region of RydC adopts a structure known as a pseudoknot and that this structure is critical for the interactions between the RydC molecules and the Hfq ring. Dimastrogiovanni et al. find that one RydC molecule interacts with one Hfq ring, and they identify the contact points between the RydC molecule and different regions of the Hfq ring.

Based on this information, Dimastrogiovanni et al. propose a model for how the RydC:Hfq complex is likely to interact with a messenger RNA molecule. The next step will be to test this model in experiments.

DOI:http://dx.doi.org/10.7554/eLife.05375.002

Identifying functionally important cis-peptide containing segments in proteins and their utility in molecular function annotation

Cis-peptide embedded segments are rare in proteins but often highlight their important role in molecular function when they do occur. The high evolutionary conservation of these segments illustrates this observation almost universally, although no attempt has been made to systematically use this information for the purpose of function annotation. In the present study, we demonstrate how geometric clustering and level-specific Gene Ontology molecular-function terms (also known as annotations) can be used in a statistically significant manner to identify cis-embedded segments in a protein linked to its molecular function. The present study identifies novel cis-peptide fragments, which are subsequently used for fragment-based function annotation. Annotation recall benchmarks interpreted using the receiver-operator characteristic plot returned an area-under-curve > 0.9, corroborating the utility of the annotation method. In addition, we identified cis-peptide fragments occurring in conjunction with functionally important trans-peptide fragments, providing additional insights into molecular function. We further illustrate the applicability of our method in function annotation where homology-based annotation transfer is not possible. The findings of the present study add to the repertoire of function annotation approaches and also facilitate engineering, design and allied studies around the cis-peptide neighborhood of proteins.

Recognition of U-rich RNA by Hfq from the Gram-positive pathogen Listeria monocytogenes

Hfq is a post-transcriptional regulator that binds U- and A-rich regions of sRNAs and their target mRNAs to stimulate their annealing in order to effect translation regulation and, often, to alter their stability. The functional importance of Hfq and its RNA-binding properties are relatively well understood in Gram-negative bacteria, whereas less is known about the RNA-binding properties of this riboregulator in Gram-positive species. Here, we describe the structure of Hfq from the Gram-positive pathogen Listeria monocytogenes in its RNA-free form and in complex with a U6 oligoribonucleotide. As expected, the protein takes the canonical hexameric toroidal shape of all other known Hfq structures. The U6 RNA binds on the "proximal face" in a pocket formed by conserved residues Q9, N42, F43, and K58. Additionally residues G5 and Q6 are involved in protein-nucleic and inter-subunit contacts that promote uracil specificity. Unlike Staphylococcus aureus (Sa) Hfq, Lm Hfq requires magnesium to bind U6 with high affinity. In contrast, the longer oligo-uridine, U16, binds Lm Hfq tightly in the presence or absence of magnesium, thereby suggesting the importance of additional residues on the proximal face and possibly the lateral rim in RNA interaction. Intrinsic tryptophan fluorescence quenching (TFQ) studies reveal, surprisingly, that Lm Hfq can bind (GU)3G and U6 on its proximal and distal faces, indicating a less stringent adenine-nucleotide specificity site on the distal face as compared to the Gram-positive Hfq proteins from Sa and Bacillus subtilis and suggesting as yet uncharacterized RNA-binding modes on both faces.

Regulation of Hfq by the RNA CrcZ in Pseudomonas aeruginosa carbon catabolite repression

Carbon Catabolite repression (CCR) allows a fast adaptation of Bacteria to changing nutrient supplies. The Pseudomonas aeruginosa (PAO1) catabolite repression control protein (Crc) was deemed to act as a translational regulator, repressing functions involved in uptake and utilization of carbon sources. However, Crc of PAO1 was recently shown to be devoid of RNA binding activity. In this study the RNA chaperone Hfq was identified as the principle post-transcriptional regulator of CCR in PAO1. Hfq is shown to bind to A-rich sequences within the ribosome binding site of the model mRNA amiE, and to repress translation in vitro and in vivo. We further report that Crc plays an unknown ancillary role, as full-fledged repression of amiE and other CCR-regulated mRNAs in vivo required its presence. Moreover, we show that the regulatory RNA CrcZ, transcription of which is augmented when CCR is alleviated, binds to Hfq with high affinity. This study on CCR in PAO1 revealed a novel concept for Hfq function, wherein the regulatory RNA CrcZ acts as a decoy to abrogate Hfq-mediated translational repression of catabolic genes and thus highlights the central role of RNA based regulation in CCR of PAO1.

Carbon assimilation in Bacteria is governed by a mechanism known as carbon catabolite repression (CCR). In contrast to several other bacterial clades CCR in Pseudomonas species appears to be primarily regulated at the post-transcriptional level. In this study, we have identified the RNA chaperone Hfq as the principle post-transcriptional regulator of CCR in P. aeruginosa (PAO1). Hfq is shown to act as a translational regulator and to prevent ribosome loading through binding to A-rich sequences within the ribosome binding site of mRNAs, which encode enzymes involved in carbon utilization. It has been previously shown that the synthesis of the RNA CrcZ is augmented in the presence of non-preferred carbon sources. Here, we show that the CrcZ RNA binds to and sequesters Hfq, which in turn abrogates Hfq-mediated translational repression of mRNAs, the encoded functions of which are required for the breakdown of non-preferred carbon sources. This novel mechanistic twist on Hfq function not only highlights the central role of RNA based regulation in CCR of PAO1 but also broadens the view of Hfq-mediated post-transcriptional mechanisms.

RNA binding by Hfq and ring-forming (L)Sm proteins: a trade-off between optimal sequence readout and RNA backbone conformation

The eukaryotic Sm and the Sm-like (LSm) proteins form a large family that includes LSm proteins in archaea and the Hfq proteins in bacteria. Commonly referred to as the (L)Sm protein family, the various members play important roles in RNA processing, decay, and riboregulation. Particularly interesting from a structural point of view is their ability to assemble into doughnut-shaped rings, which allows them to bind preferentially the uridine-rich 3′-end of RNA oligonucleotides. With an emphasis on Hfq, this review compares the RNA-binding properties of the various (L)Sm rings that were recently co-crystallized with RNA substrates, and it discusses how these properties relate to physiological function.

Mapping Hfq-RNA interaction surfaces using tryptophan fluorescence quenching

Hfq is a posttranscriptional riboregulator and RNA chaperone that binds small RNAs and target mRNAs to effect their annealing and message-specific regulation in response to environmental stressors. Structures of Hfq-RNA complexes indicate that U-rich sequences prefer the proximal face and A-rich sequences the distal face; however, the Hfq-binding sites of most RNAs are unknown. Here, we present an Hfq-RNA mapping approach that uses single tryptophan-substituted Hfq proteins, all of which retain the wild-type Hfq structure, and tryptophan fluorescence quenching (TFQ) by proximal RNA binding. TFQ properly identified the respective distal and proximal binding of A15 and U6 RNA to Gram-negative Escherichia coli (Ec) Hfq and the distal face binding of (AA)3A, (AU)3A and (AC)3A to Gram-positive Staphylococcus aureus (Sa) Hfq. The inability of (GU)3G to bind the distal face of Sa Hfq reveals the (R-L)n binding motif is a more restrictive (A-L)n binding motif. Remarkably Hfq from Gram-positive Listeria monocytogenes (Lm) binds (GU)3G on its proximal face. TFQ experiments also revealed the Ec Hfq (A-R-N)n distal face-binding motif should be redefined as an (A-A-N)n binding motif. TFQ data also demonstrated that the 5'-untranslated region of hfq mRNA binds both the proximal and distal faces of Ec Hfq and the unstructured C-terminus.